Classification of Omicron BA.1, BA.1.1, and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data

Yosuke Hirotsu; Makoto Maejima; Masahiro Shibusawa; Yume Natori; Yuki Nagakubo; Kazuhiro Hosaka; Hitomi Sueki; Hitoshi Mochizuki; Toshiharu Tsutsui; Yumiko Kakizaki; Yoshihiro Miyashita; Masao Omata

International Journal of Infectious Diseases (Sep 2022)

Classification of Omicron BA.1, BA.1.1, and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data

Yosuke Hirotsu,
Makoto Maejima,
Masahiro Shibusawa,
Yume Natori,
Yuki Nagakubo,
Kazuhiro Hosaka,
Hitomi Sueki,
Hitoshi Mochizuki,
Toshiharu Tsutsui,
Yumiko Kakizaki,
Yoshihiro Miyashita,
Masao Omata

Affiliations

Yosuke Hirotsu: Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Corresponding author: Yosuke Hirotsu, Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan, Post code: 400-8506, Tel: +81-55-253-7111; fax: +81-55-253-8011, ORCID ID: 0000-0002-8002-834X.
Makoto Maejima: Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Masahiro Shibusawa: Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Yume Natori: Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Yuki Nagakubo: Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Kazuhiro Hosaka: Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Hitomi Sueki: Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Hitoshi Mochizuki: Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Central Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Toshiharu Tsutsui: Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Yumiko Kakizaki: Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Yoshihiro Miyashita: Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Masao Omata: Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan

Journal volume & issue: Vol. 122
pp. 486 – 491

Abstract

Read online

Objectives: Recently, the Omicron strain of SARS-CoV-2 has spread and replaced the previously dominant Delta strain. Several Omicron sublineages (BA.1, BA.1.1, and BA.2) have been identified, with in vitro and preclinical reports showing that the pathogenicity and therapeutic efficacy differs between BA.1 and BA.2. We sought to develop a TaqMan assay to identify these subvariants. Methods: A TaqMan assay was constructed for rapid identification and genotyping of Omicron sublineages with 171 samples. We analyzed three characteristic mutations of the spike gene, Δ69–70, G339D, and Q493R, by TaqMan assay. The accuracy of the TaqMan assay was examined by comparing its results with the results of whole genome sequencing (WGS) analysis. Results: A total of 171 SARS-CoV-2 positive samples were analyzed by WGS and TaqMan assay. The 127 samples determined as BA.1/BA.1.1 by WGS were all positive for Δ69–70, G339D and Q493R by TaqMan assay. A total of 42 samples, determined as BA.2 by WGS, were negative for Δ69–70 but positive for G339D and Q493R by TaqMan. Two samples with G339N were determined to be inconclusive by the TaqMan method. Except for these two samples, the concordance rate between WGS and the TaqMan assay was 100% (169/169). Conclusion: TaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages.

Published in International Journal of Infectious Diseases

ISSN: 1201-9712 (Print); 1878-3511 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Medicine: Internal medicine: Infectious and parasitic diseases
Website: http://www.journals.elsevier.com/international-journal-of-infectious-diseases/

About the journal

Abstract

Keywords